-
2
-
-
0036510961
-
Identification and mapping of small-molecule binding sites in proteins: Computational tools for structure-based drug design
-
Sotriffer C., Klebe G. Identification and mapping of small-molecule binding sites in proteins: computational tools for structure-based drug design. Farmaco. 57:2002;243-251.
-
(2002)
Farmaco
, vol.57
, pp. 243-251
-
-
Sotriffer, C.1
Klebe, G.2
-
3
-
-
0029587166
-
A method to predict functional residues in proteins
-
Casari G., Sander C., Valencia A. A method to predict functional residues in proteins. Nat. Struct. Biol. 2:1995;171-178.
-
(1995)
Nat. Struct. Biol.
, vol.2
, pp. 171-178
-
-
Casari, G.1
Sander, C.2
Valencia, A.3
-
4
-
-
0034644783
-
Analysis and prediction of functional sub-types from protein sequence alignments
-
Hannenhalli S.S., Russell R.B. Analysis and prediction of functional sub-types from protein sequence alignments. J. Mol. Biol. 303:2000;61-76.
-
(2000)
J. Mol. Biol.
, vol.303
, pp. 61-76
-
-
Hannenhalli, S.S.1
Russell, R.B.2
-
5
-
-
0035853280
-
Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins
-
Landgraf R., Xenarios I., Eisenberg D. Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J. Mol. Biol. 307:2001;1487-1502.
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 1487-1502
-
-
Landgraf, R.1
Xenarios, I.2
Eisenberg, D.3
-
6
-
-
0036468670
-
Evolutionary predictions of binding surfaces and interactions
-
A thorough review of evolutionary predictions of binding surfaces and interactions, covering early and recent methods in the field. The section on evolutionary predictions in the present review follows on from the scope of this article.
-
Lichtarge O., Sowa M.E. Evolutionary predictions of binding surfaces and interactions. Curr. Opin. Struct. Biol. 12:2002;21-27 A thorough review of evolutionary predictions of binding surfaces and interactions, covering early and recent methods in the field. The section on evolutionary predictions in the present review follows on from the scope of this article.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 21-27
-
-
Lichtarge, O.1
Sowa, M.E.2
-
7
-
-
0029913807
-
An evolutionary trace method defines binding surfaces common to protein families
-
Lichtarge O., Bourne H.R., Cohen F.E. An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol. 257:1996;342-358.
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 342-358
-
-
Lichtarge, O.1
Bourne, H.R.2
Cohen, F.E.3
-
8
-
-
0035896024
-
ConSurf: An algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information
-
Armon A., Graur D., Ben-Tal N. ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J. Mol. Biol. 307:2001;447-463.
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 447-463
-
-
Armon, A.1
Graur, D.2
Ben-Tal, N.3
-
9
-
-
0035178383
-
Protein-protein interfaces: Analysis of amino acid conservation in homodimers
-
Valdar W.S., Thornton J.M. Protein-protein interfaces: analysis of amino acid conservation in homodimers. Proteins. 42:2001;108-124.
-
(2001)
Proteins
, vol.42
, pp. 108-124
-
-
Valdar, W.S.1
Thornton, J.M.2
-
10
-
-
0037693805
-
Diversity in the SH2 domain family phosphotyrosyl peptide binding site
-
Campbell S.J., Jackson R.M. Diversity in the SH2 domain family phosphotyrosyl peptide binding site. Protein Eng. 16:2003;217-227.
-
(2003)
Protein Eng.
, vol.16
, pp. 217-227
-
-
Campbell, S.J.1
Jackson, R.M.2
-
11
-
-
0002218484
-
Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
-
The authors address the issue of branching distance in the mapping of phylogenetic information to three-dimensional surfaces of proteins. Rate4Site
-
Pupko T., Bell R.E., Mayrose I., Glaser F., Ben-Tal N. Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics. 18:2002;S71-S77 The authors address the issue of branching distance in the mapping of phylogenetic information to three-dimensional surfaces of proteins. Rate4Site, a tool developed by the group, uses the maximum likelihood method to compute amino acid replacement probabilities for each branch in a phylogenetic tree. The rate of evolution is then mapped onto the surface of a representative structure.
-
(2002)
Bioinformatics
, vol.18
-
-
Pupko, T.1
Bell, R.E.2
Mayrose, I.3
Glaser, F.4
Ben-Tal, N.5
-
12
-
-
0037440008
-
Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information
-
Blouin C., Boucher Y., Roger A.J. Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information. Nucleic Acids Res. 31:2003;790-797.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 790-797
-
-
Blouin, C.1
Boucher, Y.2
Roger, A.J.3
-
13
-
-
0036145469
-
Persistently conserved positions in structurally similar, sequence dissimilar proteins: Roles in preserving protein fold and function
-
Pairs of protein families similar in structure and dissimilar in sequence are studied. Within each family, persistently conserved positions are defined as residue positions remaining conserved over several PSI-BLAST iterations (or long evolutionary times). MPC positions are those structurally aligned positions that are persistently conserved in both families. MPC positions are shown to occur frequently in key structural and functional locations, such as active sites, areas important for active site stability and the termini of helices.
-
Friedberg I., Margalit H. Persistently conserved positions in structurally similar, sequence dissimilar proteins: roles in preserving protein fold and function. Protein Sci. 11:2002;350-360 Pairs of protein families similar in structure and dissimilar in sequence are studied. Within each family, persistently conserved positions are defined as residue positions remaining conserved over several PSI-BLAST iterations (or long evolutionary times). MPC positions are those structurally aligned positions that are persistently conserved in both families. MPC positions are shown to occur frequently in key structural and functional locations, such as active sites, areas important for active site stability and the termini of helices.
-
(2002)
Protein Sci.
, vol.11
, pp. 350-360
-
-
Friedberg, I.1
Margalit, H.2
-
14
-
-
0035970287
-
Consistency analysis of similarity between multiple alignments: Prediction of protein function and fold structure from analysis of local sequence motifs
-
Kunin V., Chan B., Sitbon E., Lithwick G., Pietrokovski S. Consistency analysis of similarity between multiple alignments: prediction of protein function and fold structure from analysis of local sequence motifs. J. Mol. Biol. 307:2001;939-949.
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 939-949
-
-
Kunin, V.1
Chan, B.2
Sitbon, E.3
Lithwick, G.4
Pietrokovski, S.5
-
15
-
-
0036435908
-
Co-evolutionary analysis reveals insights into protein-protein interactions
-
Goh C.S., Cohen F.E. Co-evolutionary analysis reveals insights into protein-protein interactions. J. Mol. Biol. 324:2002;177-192.
-
(2002)
J. Mol. Biol.
, vol.324
, pp. 177-192
-
-
Goh, C.S.1
Cohen, F.E.2
-
16
-
-
0037069193
-
Inaugural article: Finding important sites in protein sequences
-
Bickel P.J., Kechris K.J., Spector P.C., Wedemayer G.J., Glazer A.N. Inaugural article: finding important sites in protein sequences. Proc. Natl. Acad. Sci. USA. 99:2002;14764-14771.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 14764-14771
-
-
Bickel, P.J.1
Kechris, K.J.2
Spector, P.C.3
Wedemayer, G.J.4
Glazer, A.N.5
-
17
-
-
0035940421
-
THEMATICS: A simple computational predictor of enzyme function from structure
-
Ondrechen M.J., Clifton J.G., Ringe D. THEMATICS: a simple computational predictor of enzyme function from structure. Proc. Natl. Acad. Sci. USA. 98:2001;12473-12478.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 12473-12478
-
-
Ondrechen, M.J.1
Clifton, J.G.2
Ringe, D.3
-
18
-
-
0035965145
-
Prediction of functionally important residues based solely on the computed energetics of protein structure
-
The author presents a method for identifying functional residues on the basis of electrostatics. It is applied to three uncharacterised structures from a structural genomics initiative, and identifies charged residues in areas of the protein surface also showing other characteristics of functional sites, including exposed hydrophobic residues and, in one case, a cluster of four cysteines that could potentially bind a metal ion. In a larger set of proteins, residues showing strong evolutionary conservation are found among either the most stabilising residues in the structure (and are therefore probably important for structural stability) or the most destabilising (and are therefore probably important for functional reasons).
-
Elcock A.H. Prediction of functionally important residues based solely on the computed energetics of protein structure. J. Mol. Biol. 312:2001;885-896 The author presents a method for identifying functional residues on the basis of electrostatics. It is applied to three uncharacterised structures from a structural genomics initiative, and identifies charged residues in areas of the protein surface also showing other characteristics of functional sites, including exposed hydrophobic residues and, in one case, a cluster of four cysteines that could potentially bind a metal ion. In a larger set of proteins, residues showing strong evolutionary conservation are found among either the most stabilising residues in the structure (and are therefore probably important for structural stability) or the most destabilising (and are therefore probably important for functional reasons).
-
(2001)
J. Mol. Biol.
, vol.312
, pp. 885-896
-
-
Elcock, A.H.1
-
19
-
-
0036435882
-
Analysis of catalytic residues in enzyme active sites
-
A thorough study of the properties of catalytic residues in protein structures. Six amino acid residues (histidine, cysteine, aspartic acid, glutamic acid, arginine and lysine) are shown to account for 70% of all catalytic residues. These tend to be strongly conserved, have low crystallographic B-factors (indicating low structural flexibility) and make correspondingly high numbers of hydrogen bonds. Interestingly, glycine accounts for a large proportion of residues involved in catalysis using mainchain atoms.
-
Bartlett G.J., Porter C.T., Borkakoti N., Thornton J.M. Analysis of catalytic residues in enzyme active sites. J. Mol. Biol. 324:2002;105-121 A thorough study of the properties of catalytic residues in protein structures. Six amino acid residues (histidine, cysteine, aspartic acid, glutamic acid, arginine and lysine) are shown to account for 70% of all catalytic residues. These tend to be strongly conserved, have low crystallographic B-factors (indicating low structural flexibility) and make correspondingly high numbers of hydrogen bonds. Interestingly, glycine accounts for a large proportion of residues involved in catalysis using mainchain atoms.
-
(2002)
J. Mol. Biol.
, vol.324
, pp. 105-121
-
-
Bartlett, G.J.1
Porter, C.T.2
Borkakoti, N.3
Thornton, J.M.4
-
20
-
-
0035815113
-
Evolution of function in protein superfamilies, from a structural perspective
-
Todd A.E., Orengo C.A., Thornton J.M. Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307:2001;1113-1143.
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 1113-1143
-
-
Todd, A.E.1
Orengo, C.A.2
Thornton, J.M.3
-
21
-
-
0034308142
-
Practical limits of function prediction
-
Devos D., Valencia A. Practical limits of function prediction. Proteins. 41:2000;98-107.
-
(2000)
Proteins
, vol.41
, pp. 98-107
-
-
Devos, D.1
Valencia, A.2
-
22
-
-
0036384350
-
One fold with many functions: The evolutionary relationships between TIM barrel families based on their sequences, structures and functions
-
Nagano N., Orengo C.A., Thornton J.M. One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J. Mol. Biol. 321:2002;741-765.
-
(2002)
J. Mol. Biol.
, vol.321
, pp. 741-765
-
-
Nagano, N.1
Orengo, C.A.2
Thornton, J.M.3
-
23
-
-
0036169142
-
LigBase: A database of families of aligned ligand binding sites in known protein sequences and structures
-
Stuart A.C., Ilyin V.A., Sali A. LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures. Bioinformatics. 18:2002;200-201.
-
(2002)
Bioinformatics
, vol.18
, pp. 200-201
-
-
Stuart, A.C.1
Ilyin, V.A.2
Sali, A.3
-
24
-
-
0035782660
-
Enhanced functional annotation of protein sequences via the use of structural descriptors
-
Di Gennaro J.A., Siew N., Hoffman B.T., Zhang L., Skolnick J., Neilson L.I., Fetrow J.S. Enhanced functional annotation of protein sequences via the use of structural descriptors. J. Struct. Biol. 134:2001;232-245.
-
(2001)
J. Struct. Biol.
, vol.134
, pp. 232-245
-
-
Di Gennaro, J.A.1
Siew, N.2
Hoffman, B.T.3
Zhang, L.4
Skolnick, J.5
Neilson, L.I.6
Fetrow, J.S.7
-
25
-
-
0034651543
-
When fold is not important: A common structural framework for adenine and AMP binding in 12 unrelated protein families
-
Denessiouk K.A., Johnson M.S. When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families. Proteins. 38:2000;310-326.
-
(2000)
Proteins
, vol.38
, pp. 310-326
-
-
Denessiouk, K.A.1
Johnson, M.S.2
-
26
-
-
0035882572
-
Adenine recognition: A motif present in ATP-, CoA-, NAD-, NADP-, and FAD-dependent proteins
-
Denessiouk K.A., Rantanen V.V., Johnson M.S. Adenine recognition: a motif present in ATP-, CoA-, NAD-, NADP-, and FAD-dependent proteins. Proteins. 44:2001;282-291.
-
(2001)
Proteins
, vol.44
, pp. 282-291
-
-
Denessiouk, K.A.1
Rantanen, V.V.2
Johnson, M.S.3
-
27
-
-
0035850756
-
A fragment library based on Gaussian mixtures predicting favorable molecular interactions
-
A new approach to the distribution of protein atom types around defined ligand fragments using a Bayesian approach with Gaussian mixture models. Maximum likelihood parameters of the models are estimated using an expectation maximisation algorithm. The method gives predictions of which protein atoms interact with particular ligand fragments (example protein atoms would be 'mainchain carbonyl oxygen' or 'sidechain hydroxyl oxygen). A detailed analysis of the errors made in predictions shows that the method can effectively narrow down the set of possible interactions for ligand functional groups.
-
Rantanen V.V., Denessiouk K.A., Gyllenberg M., Koski T., Johnson M.S. A fragment library based on Gaussian mixtures predicting favorable molecular interactions. J. Mol. Biol. 313:2001;197-214 A new approach to the distribution of protein atom types around defined ligand fragments using a Bayesian approach with Gaussian mixture models. Maximum likelihood parameters of the models are estimated using an expectation maximisation algorithm. The method gives predictions of which protein atoms interact with particular ligand fragments (example protein atoms would be 'mainchain carbonyl oxygen' or 'sidechain hydroxyl oxygen). A detailed analysis of the errors made in predictions shows that the method can effectively narrow down the set of possible interactions for ligand functional groups.
-
(2001)
J. Mol. Biol.
, vol.313
, pp. 197-214
-
-
Rantanen, V.V.1
Denessiouk, K.A.2
Gyllenberg, M.3
Koski, T.4
Johnson, M.S.5
-
28
-
-
0035861977
-
Recognition templates for predicting adenylate-binding sites in proteins
-
An approach to the development of three-dimensional templates for binding site recognition. In contrast to other approaches involving the residues and chemical groups flanking the site, these templates describe the energetic properties of the ligand-binding volume by employing grid-based affinity potentials. Consensus features of these potentials are extracted from diverse structures binding the same ligand. The templates are better able to distinguish adenylate- and guanylate-binding sites than traditional energy calculation or ligand docking.
-
Zhao S., Morris G.M., Olson A.J., Goodsell D.S. Recognition templates for predicting adenylate-binding sites in proteins. J. Mol. Biol. 314:2001;1245-1255 An approach to the development of three-dimensional templates for binding site recognition. In contrast to other approaches involving the residues and chemical groups flanking the site, these templates describe the energetic properties of the ligand-binding volume by employing grid-based affinity potentials. Consensus features of these potentials are extracted from diverse structures binding the same ligand. The templates are better able to distinguish adenylate- and guanylate-binding sites than traditional energy calculation or ligand docking.
-
(2001)
J. Mol. Biol.
, vol.314
, pp. 1245-1255
-
-
Zhao, S.1
Morris, G.M.2
Olson, A.J.3
Goodsell, D.S.4
-
29
-
-
0036406643
-
A new method to detect related function among proteins independent of sequence and fold homology
-
A database of three-dimensional cavities, extracted from the Protein Data Bank, is employed. These are described in terms of the physico-chemical characteristics (e.g. hydrogen-bond donor/acceptor, whether aliphatic) of the chemical groups flanking the cavity. A clique-detection-based similarity search algorithm is shown to be able to detect and rank database entries with similar function (binding the same or similar ligands, or with similar catalytic mechanisms) for several example query cavities, independently of fold homology. The method can also be used as an idea generator for de novo drug design.
-
Schmitt S., Kuhn D., Klebe G. A new method to detect related function among proteins independent of sequence and fold homology. J. Mol. Biol. 323:2002;387-406 A database of three-dimensional cavities, extracted from the Protein Data Bank, is employed. These are described in terms of the physico-chemical characteristics (e.g. hydrogen-bond donor/acceptor, whether aliphatic) of the chemical groups flanking the cavity. A clique-detection-based similarity search algorithm is shown to be able to detect and rank database entries with similar function (binding the same or similar ligands, or with similar catalytic mechanisms) for several example query cavities, independently of fold homology. The method can also be used as an idea generator for de novo drug design.
-
(2002)
J. Mol. Biol.
, vol.323
, pp. 387-406
-
-
Schmitt, S.1
Kuhn, D.2
Klebe, G.3
-
30
-
-
0036288284
-
Identification of protein functions from a molecular surface database, eF-site
-
Kinoshita K., Furui J., Nakamura H. Identification of protein functions from a molecular surface database, eF-site. J. Struct. Funct. Genomics. 2:2001;9-22.
-
(2001)
J. Struct. Funct. Genomics
, vol.2
, pp. 9-22
-
-
Kinoshita, K.1
Furui, J.2
Nakamura, H.3
-
32
-
-
0035416126
-
High-throughput docking for lead generation
-
Abagyan R., Totrov M. High-throughput docking for lead generation. Curr. Opin. Chem. Biol. 5:2001;375-382.
-
(2001)
Curr. Opin. Chem. Biol.
, vol.5
, pp. 375-382
-
-
Abagyan, R.1
Totrov, M.2
-
33
-
-
0036137713
-
Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock
-
Osterberg F., Morris G.M., Sanner M.F., Olson A.J., Goodsell D.S. Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins. 46:2002;34-40.
-
(2002)
Proteins
, vol.46
, pp. 34-40
-
-
Osterberg, F.1
Morris, G.M.2
Sanner, M.F.3
Olson, A.J.4
Goodsell, D.S.5
-
34
-
-
0036084259
-
Efficient docking of peptides to proteins without prior knowledge of the binding site
-
Hetenyi C., van der Spoel D. Efficient docking of peptides to proteins without prior knowledge of the binding site. Protein Sci. 11:2002;1729-1737.
-
(2002)
Protein Sci.
, vol.11
, pp. 1729-1737
-
-
Hetenyi, C.1
Van Der Spoel, D.2
-
35
-
-
0037057576
-
Docking of flexible molecules using multiscale ligand representations
-
The number of feature points are progressively increased during the simulation and different conformations clustered to remove redundancy at a given level of feature points. This produces a hierarchy of models for the ligand, which are clustered and then pruned at each successive level, ultimately producing an all-atom ligand representation.
-
Glick M., Grant G.H., Richards W.G. Docking of flexible molecules using multiscale ligand representations. J. Med. Chem. 45:2002;4639-4646 The number of feature points are progressively increased during the simulation and different conformations clustered to remove redundancy at a given level of feature points. This produces a hierarchy of models for the ligand, which are clustered and then pruned at each successive level, ultimately producing an all-atom ligand representation.
-
(2002)
J. Med. Chem.
, vol.45
, pp. 4639-4646
-
-
Glick, M.1
Grant, G.H.2
Richards, W.G.3
-
36
-
-
0036022961
-
Q-fit: A probabilistic method for docking molecular fragments by sampling low energy conformational space
-
The receptor binding site is 'probed' before docking. Receptor binding modes are defined in three dimensions in terms of a triplet of receptor probes that potentially correspond to atom triplets in the ligand. The ranking of these triplets by energy allows an ordered search of binding modes, so that those with the lowest energy are sampled first.
-
Jackson R.M. Q-fit: a probabilistic method for docking molecular fragments by sampling low energy conformational space. J. Comput. Aided Mol. Des. 16:2002;43-57 The receptor binding site is 'probed' before docking. Receptor binding modes are defined in three dimensions in terms of a triplet of receptor probes that potentially correspond to atom triplets in the ligand. The ranking of these triplets by energy allows an ordered search of binding modes, so that those with the lowest energy are sampled first.
-
(2002)
J. Comput. Aided Mol. Des.
, vol.16
, pp. 43-57
-
-
Jackson, R.M.1
-
37
-
-
0036882099
-
Enhanced docking with the mining minima optimizer: Acceleration and side-chain flexibility
-
Kairys V., Gilson M.K. Enhanced docking with the mining minima optimizer: acceleration and side-chain flexibility. J. Comput. Chem. 23:2002;1656-1670.
-
(2002)
J. Comput. Chem.
, vol.23
, pp. 1656-1670
-
-
Kairys, V.1
Gilson, M.K.2
-
38
-
-
0035976367
-
EUDOC: A computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases
-
Pang Y.P., Perola E., Xu K., Prendergast F.G. EUDOC: a computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases. J. Comput. Chem. 22:2001;1750-1771.
-
(2001)
J. Comput. Chem.
, vol.22
, pp. 1750-1771
-
-
Pang, Y.P.1
Perola, E.2
Xu, K.3
Prendergast, F.G.4
-
39
-
-
0036147568
-
Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations
-
Ma B., Shatsky M., Wolfson H.J., Nussinov R. Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci. 11:2002;184-197.
-
(2002)
Protein Sci.
, vol.11
, pp. 184-197
-
-
Ma, B.1
Shatsky, M.2
Wolfson, H.J.3
Nussinov, R.4
-
40
-
-
0036323965
-
Ligand-induced changes in the binding sites of proteins
-
Fradera X., De La Cruz X., Silva C.H., Gelpi J.L., Luque F.J., Orozco M. Ligand-induced changes in the binding sites of proteins. Bioinformatics. 18:2002;939-948.
-
(2002)
Bioinformatics
, vol.18
, pp. 939-948
-
-
Fradera, X.1
De La Cruz, X.2
Silva, C.H.3
Gelpi, J.L.4
Luque, F.J.5
Orozco, M.6
-
41
-
-
0037125501
-
Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach
-
Kua J., Zhang Y., McCammon J.A. Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach. J. Am. Chem. Soc. 124:2002;8260-8267.
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 8260-8267
-
-
Kua, J.1
Zhang, Y.2
McCammon, J.A.3
-
42
-
-
0035957528
-
FlexE: Efficient molecular docking considering protein structure variations
-
Claussen H., Buning C., Rarey M., Lengauer T. FlexE: efficient molecular docking considering protein structure variations. J. Mol. Biol. 308:2001;377-395.
-
(2001)
J. Mol. Biol.
, vol.308
, pp. 377-395
-
-
Claussen, H.1
Buning, C.2
Rarey, M.3
Lengauer, T.4
-
43
-
-
0035896038
-
Docking ligands onto binding site representations derived from proteins built by homology modelling
-
Ligands are aligned relative to each other to create a three-dimensional QSAR model, which is then aligned with the model protein binding site. Soft (Gaussian) functions are used for both representations and then the alignment optimises the overlap between them. The aim is to ultimately use this information to constrain the model-built structure in the modelling step via feedback between the protein and the QSAR models.
-
Schafferhans A., Klebe G. Docking ligands onto binding site representations derived from proteins built by homology modelling. J. Mol. Biol. 307:2001;407-427 Ligands are aligned relative to each other to create a three-dimensional QSAR model, which is then aligned with the model protein binding site. Soft (Gaussian) functions are used for both representations and then the alignment optimises the overlap between them. The aim is to ultimately use this information to constrain the model-built structure in the modelling step via feedback between the protein and the QSAR models.
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 407-427
-
-
Schafferhans, A.1
Klebe, G.2
-
44
-
-
0036022958
-
Flexible docking under pharmacophore-type constraints
-
The method applies a series of look-ahead checks to see if a currently generated solution obeys the pharmacophore constraints and removes those that do not. This can speed up calculation times.
-
Hindle S.A., Rarey M., Buning C., Lengaue T. Flexible docking under pharmacophore-type constraints. J. Comput. Aided. Mol. Des. 16:2002;129-149 The method applies a series of look-ahead checks to see if a currently generated solution obeys the pharmacophore constraints and removes those that do not. This can speed up calculation times.
-
(2002)
J. Comput. Aided. Mol. Des.
, vol.16
, pp. 129-149
-
-
Hindle, S.A.1
Rarey, M.2
Buning, C.3
Lengaue, T.4
-
45
-
-
0037083321
-
Docking multiple conformations of a flexible ligand into a protein binding site using NMR restraints
-
Zabell A.P., Post C.B. Docking multiple conformations of a flexible ligand into a protein binding site using NMR restraints. Proteins. 46:2002;295-307.
-
(2002)
Proteins
, vol.46
, pp. 295-307
-
-
Zabell, A.P.1
Post, C.B.2
-
46
-
-
0035312864
-
Statistical potentials and scoring functions applied to protein-ligand binding
-
Gohlke H., Klebe G. Statistical potentials and scoring functions applied to protein-ligand binding. Curr. Opin. Struct. Biol. 11:2001;231-235.
-
(2001)
Curr. Opin. Struct. Biol.
, vol.11
, pp. 231-235
-
-
Gohlke, H.1
Klebe, G.2
-
47
-
-
0036022960
-
Further development and validation of empirical scoring functions for structure-based binding affinity prediction
-
Wang R., Lai L., Wang S. Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J. Comput. Aided. Mol. Des. 16:2002;11-26.
-
(2002)
J. Comput. Aided. Mol. Des.
, vol.16
, pp. 11-26
-
-
Wang, R.1
Lai, L.2
Wang, S.3
-
48
-
-
0037068492
-
DrugScore meets CoMFA: Adaptation of fields for molecular comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein
-
Experimental protein-ligand binding affinities are used as a training set to adapt the DrugScore function to a particular protein. This tailor-made scoring function improves the predictive power for affinity prediction in the two proteins studied.
-
Gohlke H., Klebe G. DrugScore meets CoMFA: adaptation of fields for molecular comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein. J. Med. Chem. 45:2002;4153-4170 Experimental protein-ligand binding affinities are used as a training set to adapt the DrugScore function to a particular protein. This tailor-made scoring function improves the predictive power for affinity prediction in the two proteins studied.
-
(2002)
J. Med. Chem.
, vol.45
, pp. 4153-4170
-
-
Gohlke, H.1
Klebe, G.2
-
49
-
-
0035966871
-
Detailed analysis of scoring functions for virtual screening
-
Stahl M., Rarey M. Detailed analysis of scoring functions for virtual screening. J. Med. Chem. 44:2001;1035-1042.
-
(2001)
J. Med. Chem.
, vol.44
, pp. 1035-1042
-
-
Stahl, M.1
Rarey, M.2
-
50
-
-
0035829446
-
Evaluation of docking functions for protein-ligand docking
-
Perez C., Ortiz A.R. Evaluation of docking functions for protein-ligand docking. J. Med. Chem. 44:2001;3768-3785.
-
(2001)
J. Med. Chem.
, vol.44
, pp. 3768-3785
-
-
Perez, C.1
Ortiz, A.R.2
-
51
-
-
0037046545
-
Docking into knowledge-based potential fields: A comparative evaluation of DrugScore
-
Sotriffer C.A., Gohlke H., Klebe G. Docking into knowledge-based potential fields: a comparative evaluation of DrugScore. J. Med. Chem. 45:2002;1967-1970.
-
(2002)
J. Med. Chem.
, vol.45
, pp. 1967-1970
-
-
Sotriffer, C.A.1
Gohlke, H.2
Klebe, G.3
-
52
-
-
0036606204
-
ConsDock: A new program for the consensus analysis of protein-ligand interactions
-
Paul N., Rognan D. ConsDock: A new program for the consensus analysis of protein-ligand interactions. Proteins. 47:2002;521-533.
-
(2002)
Proteins
, vol.47
, pp. 521-533
-
-
Paul, N.1
Rognan, D.2
-
53
-
-
0013133162
-
A new test set for validating predictions of protein-ligand interaction
-
Nissink J.W., Murray C., Hartshorn M., Verdonk M.L., Cole J.C., Taylor R. A new test set for validating predictions of protein-ligand interaction. Proteins. 49:2002;457-471.
-
(2002)
Proteins
, vol.49
, pp. 457-471
-
-
Nissink, J.W.1
Murray, C.2
Hartshorn, M.3
Verdonk, M.L.4
Cole, J.C.5
Taylor, R.6
-
54
-
-
0035950051
-
Ligand-protein database: Linking protein-ligand complex structures to binding data
-
Roche O., Kiyama R., Brooks C.L. III Ligand-protein database: linking protein-ligand complex structures to binding data. J. Med. Chem. 44:2001;3592-3598.
-
(2001)
J. Med. Chem.
, vol.44
, pp. 3592-3598
-
-
Roche, O.1
Kiyama, R.2
Brooks C.L. III3
|